Mobilization of seed storage proteins is crucial to high vigor in common bean seeds / Mobilização das proteínas de reserva é crucial para o alto vigor em sementes de feijão

Seed germination is a complex process controlled by many factors, in which physical and biochemical mechanisms are involved and the mobilization of reserves is crucial for this process to occur. Although, seed reserve mobilization is usually thought to be a post-germination process, seed reserve proteins mobilization occurs during germination. This study quantified seed proteins of bean genotypes during different hydration times, in order to understand the process of protein mobilization and whether there is relationship of this biochemical component with seed vigor. This study was conducted using seeds with different levels of vigor, genotypes with highest (13, 42, 55 and 81) and lowest (07, 23, 44, 50, IPR-88-Uirapurú and Iapar 81) physiological quality. High vigor genotypes showed greater efficiency in hydrolysis and mobilization of protein component, because they presented low globulins content in cotyledons at radicle protrusion in relation to low vigor genotypes (07, 23 and 50). The protein alpha-amylase inhibitor, observed in all genotypes, is involved with the longer time needed for radicle protrusion, according to the band intensity difference in genotypes 07, 44 and Iapar 81.

A germinação de sementes é um processo complexo controlado por muitos fatores, nos quais mecanismos físicos e bioquímicos estão envolvidos e a mobilização de reservas é decisiva para que esse processo ocorra. Embora a mobilização de reservas de sementes seja considerada um processo pós-germinativo, a mobilização das proteínas de reserva de sementes ocorre durante a germinação. Este estudo teve como objetivo quantificar as proteínas de sementes de genótipos de feijão durante os diferentes tempos de hidratação, a fim de compreender o processo de mobilização proteica e se há relação desse componente bioquímico com o vigor das sementes. Este estudo foi realizado utilizando sementes com diferentes níveis de vigor, genótipos com maior (13, 42, 55 e 81) e menor (07, 23, 44, 50, IPR-88-Uirapurú e Iapar 81) qualidade fisiológica. Os genótipos de alto vigor apresentaram maior eficiência na hidrólise e mobilização do componente proteico, pois apresentaram baixo teor de globulinas nos cotilédones na protrusão radicular em relação aos genótipos de baixo vigor (07, 23 e 50). A proteína inibidora da alfa-amilase, observada em todos os genótipos, está envolvida com o maior tempo necessário para a protrusão da radícula, de acordo com a diferença de intensidade da banda nos genótipos 07, 44 e Iapar 81.

Genome-wide association studies of Ca and Mn in the seeds of the common bean (Phaseolus vulgaris L.).

SNP markers linked to genes controlling Ca and Mn uptake were identified in the common bean seeds using DArT-based association mapping (AM). The Ca concentration in the seeds varied between 475 and 3,100 mg kg-1 with an average of 1,280.9 mg kg-1 and the Mn concentration ranged from 4.87 to 27.54 mg kg-1 with a mean of 11.76 mg kg-1. A total of 19,204 SNP markers were distributed across 11 chromosomes that correspond to the haploid genome number of the common bean. The highest value of ΔK was determined as K = 2, and 173 common bean genotypes were split into two main subclusters as POP1 (Mesoamerican) and POP2 (Andean). The results of the UPGMA dendrogram and PCA confirmed those of STRUCTURE analysis. MLM based on the Q + K model identified a large number of markers-trait associations. Of the 19,204 SNPs, five (on Pv2, 3, 8, 10 and 11) and four (on Pv2, 3, 8 and 11) SNPs were detected to be significantly related to the Ca content of the beans grown in Bornova and Menemen, respectively in 2015. In 2016, six SNPs (on Pv1-4, 8 and 10) were identified to be significantly associated with the Ca content of the seeds obtained from Bornova and six SNPs (on Pv1-4, 8 and 10) from Menemen. Eight (on Pv3, 5 and 11) and four (on Pv2, 5 and 11) SNPs had a significant association with Mn content in Bornova in 2015 and 2016, respectively. In Menemen, eight (on Pv3, 5, 8 and 11) and 11 (on Pv1, 2, 5, 10 and 11) SNPs had a significant correlation with Mn content in 2015 and 2016, respectively.

Using Giant Scarlet Runner Bean (Phaseolus coccineus) Embryos to Dissect the Early Events in Plant Embryogenesis.

The giant embryo of the scarlet runner bean (Phaseolus coccineus) has been used historically to investigate the molecular and developmental processes that control the early events of plant embryo development. In more recent years, our laboratory has been using scarlet runner bean embryos to uncover the genes and regulatory events that control embryo proper and suspensor region differentiation shortly after fertilization. In this chapter we describe methods that we have developed to isolate scarlet runner bean embryos at the globular stage of development, and capture embryo proper and suspensor regions by either hand dissection or laser capture microdissection (LCM) for use in downstream genomic analysis. These methods are also applicable for use in investigating the early events of common bean (Phaseolus vulgaris) embryo development, a close relative of scarlet runner bean, which also has a giant embryo in addition to a sequenced genome.

Somatic Embryogenesis in Common BeanPhaseolus vulgaris L.

Common bean Phaseolus vulgaris L. has been shown to be a recalcitrant plant to induce somatic embryogenesis (SE) under in vitro conditions. An alternative strategy to yield SE is based upon the use of a cytokinin (benzyladenine) coupled with osmotic stress adaptation instead of the auxin-inducing SE in common bean. Here we described the induction of proembryogenic masses (PEM) derived from the apical meristem and cotyledonary zone of zygotic embryos, from which secondary SE indirect embryogenesis emerged. Maturation of SE was achieved by using osmotic stress medium and converted to plants. Long-term recurrent SE was demonstrated by propagation of PEM at early stages of SE. This protocol is currently being applied for stable genetic transformation by means of Agrobacterium tumefaciens and biobalistics as well as basic biochemical and molecular biology research.

Co-plantation of aquatic macrophytes Typha angustifolia and Paspalum scrobiculatum for effective treatment of textile industry effluent.

Field treatment of textile industry effluent was carried out in constructed drenches (91.4m×1.2m×0.6m; 65.8m3) planted independently with Typha angustifolia, Paspalum scrobiculatum and their co-plantation (consortium-TP). The in situ treatment of effluent by T. angustifolia, P. scrobiculatum and consortium-TP was found to decrease ADMI color value by 62, 59 and 76%, COD by 65, 63 and 70%, BOD by 68, 63 and 75%, TDS by 45, 39 and 57%, and TSS by 35, 31 and 47%, respectively within 96h. Heavy metals such as arsenic, cadmium, chromium and lead were also removed up to 28-77% after phytoremediation. T. angustifolia and P. scrobiculatum showed removal of Congo Red (100mg/L) up to 80 and 73%, respectively within 48h while consortium-TP achieved 94% decolorization. Root tissues of T. angustifolia and P. scrobiculatum revealed inductions in the activities of oxido-reductive enzymes such as lignin peroxidase (193 and 32%), veratryl alcohol oxidase (823 and 460%), laccase (492 and 182%) and azo reductase (248 and 83%), respectively during decolorization of Congo Red. Anatomical studies of roots, FTIR, HPLC, UV-vis Spectroscopy and GC-MS analysis verified the phytotransformation. Phytotoxicity studies confirmed reduced toxicity of the metabolites of Congo Red.

Differential proteomics reveals the hallmarks of seed development in common bean (Phaseolus vulgaris L.).

UNLABELLED: Common bean (Phaseolus vulgaris L.) is one of the most consumed staple foods worldwide. Little is known about the molecular mechanisms controlling seed development. This study aims to comprehensively describe proteome dynamics during seed development of common bean. A high-throughput gel-free proteomics approach (LC-MS/MS) was conducted on seeds at 10, 20, 30 and 40days after anthesis, spanning from late embryogenesis until desiccation. Of the 418 differentially accumulated proteins identified, 255 were characterized, most belonging to protein metabolism. An accumulation of proteins belonging to the MapMan functional categories of "protein", "glycolysis", "TCA", "DNA", "RNA", "cell" and "stress" were found at early seed development stages, reflecting an extensive metabolic activity. In the mid stages, accumulation of storage, signaling, starch synthesis and cell wall-related proteins stood out. In the later stages, an increase in proteins related to redox, protein degradation/modification/folding and nucleic acid metabolisms reflect that seed desiccation-resistance mechanisms were activated. Our study unveils new clues to understand the regulation of seed development mediated by post-translational modifications and maintenance of genome integrity. This knowledge enhances the understanding on seed development molecular mechanisms that may be used in the design and selection of common bean seeds with desired quality traits. SIGNIFICANCE: Common bean (P. vulgaris) is an important source of proteins and carbohydrates worldwide. Despite the agronomic and economic importance of this pulse, knowledge on common bean seed development is limited. Herein, a gel-free high throughput methodology was used to describe the proteome changes during P. vulgaris seed development. Data obtained will enhance the knowledge on the molecular mechanisms controlling this grain legume seed development and may be used in the design and selection of common bean seeds with desired quality traits. Results may be extrapolated to other pulses.

Evaluating two-dimensional electrophoresis profiles of the protein phaseolin as markers of genetic differentiation and seed protein quality in common bean (Phaseolus vulgaris L.).

High-resolution two-dimensional electrophoresis (2-DE) profiles of the protein phaseolin, the major seed storage protein of common bean, display great number of spots with differentially glycosylated and phosphorylated α- and ß-type polypeptides. This work aims to test whether these complex profiles can be useful markers of genetic differentiation and seed protein quality in bean populations. The 2-DE phaseolin profile and the amino acid composition were examined in bean seeds from 18 domesticated and wild accessions belonging to the Mesoamerican and Andean gene pools. We found that proteomic distances based on 2-DE profiles were successful in identifying the accessions belonging to each gene pool and outliers distantly related. In addition, accessions identified as outliers from proteomic distances showed the highest levels of methionine content, an essential amino acid deficient in bean seeds. These findings suggest that 2-DE phaseolin profiles provide valuable information with potential of being used in common bean genetic improvement.

Purification, biochemical characterization, and bioactive properties of a lectin purified from the seeds of white tepary bean (phaseolus acutifolius variety latifolius).

The present work shows the characterization of Phaseolus acutifolius variety latifolius, on which little research has been published, and provides detailed information on the corresponding lectin. This protein was purified from a semi-domesticated line of white tepary beans from Sonora, Mexico, by precipitation of the aqueous extract with ammonium sulfate, followed by affinity chromatography on an immobilized fetuin matrix. MALDI TOF analysis of Phaseolus acutifolius agglutinin (PAA) showed that this lectin is composed of monomers with molecular weights ranging between 28 and 31 kDa. At high salt concentrations, PAA forms a dimer of 63 kDa, but at low salt concentrations, the subunits form a tetramer. Analysis of PAA on 2D-PAGE showed that there are mainly three types of subunits with isoelectric points of 4.2, 4.4, and 4.5. The partial sequence obtained by LC/MS/MS of tryptic fragments from the PAA subunits showed 90-100% identity with subunits from genus Phaseolus lectins in previous reports. The tepary bean lectin showed lower hemagglutination activity than Phaseolus vulgaris hemagglutinin (PHA-E) toward trypsinized human A and O type erythrocytes. The hemagglutination activity was inhibited by N-glycans from glycoproteins. Affinity chromatography with the immobilized PAA showed a high affinity to glycopeptides from thyroglobulin, which also has N-glycans with a high content of N-acetylglucosamine. PAA showed less mitogenic activity toward human lymphocytes than PHA-L and Con A. The cytotoxicity of PAA was determined by employing three clones of the 3T3 cell line, demonstrating variability among the clones as follows: T4 (DI50 51.5 µg/mL); J20 (DI50 275 µg/mL), and N5 (DI50 72.5 µg/mL).

Phaseolus immature embryo rescue technology.

Predominant among the production constraints of the common bean Phaseolus vulgaris are infestation of Ascochyta blight, Bean Golden Mosaic virus (BGMV), and Bean Fly. Interbreeding with Phaseolus -coccineus L. and/or Phaseolus polyanthus Greenm has been shown to provide P. vulgaris with greater resistance to these diseases. For interspecific crosses to be successful, it is important to use P. coccineus and P. polyanthus as female parents; this prevents rapid reversal to the recurrent parent P. vulgaris. Although incompatibility barriers are post-zygotic, early hybrid embryo abortion limits the success of F1 crosses. While rescue techniques for globular and early heart-shaped embryos have improved in recent years, -success in hybridization remains very low. In this study, we describe six steps that allowed us to rescue 2-day-old P. vulgaris embryos using a pod culture technique. Our methods consisted of (i) pod culture, (ii) extraction and culture of immature embryos, (iii) dehydration of embryos, (iv) germination of embryos, (v) rooting of developed shoots, and (vi) hardening of plantlets.

Unsuitable availability of nutrients in germinating bean embryos exposed to copper excess.

The influence of copper excess on germination rate, growth, minerals, carbohydrates, and amino acids supply in embryonic axis of bean seed was investigated. Compared to the control, Cu treatment caused a reduction in germination percent, embryo length, and accumulation of Ca, Fe, K, Mn, Zn, total soluble sugars, glucose, fructose, sucrose, and amino acids. Moreover, the nutrient concentrations, as well as the electrical conductivity were determined in the germination medium to quantify the extent of solute leakage. Such nutrients were lost in the imbibition medium at the expense of suitable mobilization to the growing embryonic axis. This was associated with an enhancement in accumulation of malondialdehyde, major product of lipoperoxidation process which can be due to the stimulation in lipoxygenase activity in Cu-poisoned tissues.

Germination behavior, biochemical features and sequence analysis of the RACK1/arcA homolog from Phaseolus vulgaris.

Partial peptide sequence of a 36 kDa protein from common bean embryo axes showed 100% identity with a reported beta-subunit of a heterotrimeric G protein from soybean. Analysis of the full sequence showed 96.6% identity with the reported soybean G(beta)-subunit, 86% with RACK1B and C from Arabidopsis and 66% with human and mouse RACK1, at the amino acid level. In addition, it showed 85.5, 85 and 83% identities with arcA from Solanum lycopersicum, Arabidopsis (RACK1A) and Nicotiana tabacum, respectively. The amino acid sequence displayed seven WD40 domains and two sites for activated protein kinase C binding. The protein showed a constant expression level but the mRNA had a maximum at 32 h post-imbibition. Western immunoblotting showed the protein in vegetative plant tissues, and in both microsomal and soluble fractions from embryo axes. Synthetic auxin treatment during germination delayed the peak of RACK1 mRNA expression to 48 h but did not affect the protein expression level while the polar auxin transport inhibitor, naphtylphtalamic acid had no effect on either mRNA or protein expression levels. Southern blot and genomic DNA amplification revealed a small gene family with at least one member without introns in the genome. Thus, the RACK1/arcA homolog from common bean has the following features: (1) it is highly conserved; (2) it is both soluble and insoluble within the embryo axis; (3) it is encoded by a small gene family; (4) its mRNA has a peak of expression at the time point of germination stop and (5) its expression is only slightly affected by auxin but unaffected by an auxin transport blocker.

Expression and interaction of the CBLs and CIPKs from immature seeds of kidney bean (Phaseolus vulgaris L.).

Protein phosphorylation plays a key regulatory role in a variety of cellular processes. To better understand the function of protein phosphorylation in seed maturation, a PCR-based cloning method was employed and five cDNA clones (pvcipk1-5) for protein kinases were isolated from a cDNA library prepared from immature seeds of kidney bean (Phaseolus vulgaris L.). The deduced amino acid sequences showed that the five protein kinases (PvCIPK1-5) are members of the sucrose non-fermenting 1-related protein kinase type 3 (SnRK3) family, which interacts with calcineurin B-like proteins (CBLs). Two cDNA clones (pvcbl1 and 2) for CBLs were further isolated from the cDNA library. The predicted primary sequences of the proteins (PvCBL1 and 2) displayed significant identity (more than 90%) with those of other plant CBLs. Semi-quantitative RT-PCR analysis showed that the isolated genes, except pvcbl1, are expressed in leaves and early maturing seeds, whereas pvcbl1 is constitutively expressed during seed development. Yeast two-hybrid assay indicated that among the five PvCIPKs, only PvCIPK1 interacts with both PvCBL1 and PvCBL2. These results suggest that calcium-dependent protein phosphorylation-signaling via CBL-CIPK complexes occurs during seed development.

Ureide metabolism during seedling development in French bean (Phaseolus vulgaris).

French bean (Phaseolus vulgaris) is a legume that transports most of the atmospheric nitrogen fixed in its nodules to the aerial parts of the plant as ureides. Changes in ureide content and in enzymatic activities involved in their metabolism were identified in the cotyledons and embryonic axes during germination and early seedling development. Accumulation of ureides (ca. 1300 nmol per pair of cotyledons) was observed in the cotyledons of dry seeds. Throughout germination, the total amount of ureides slightly decreased to about 1200 nmol, but increased both in cotyledons and in embryonic axes after radicle emergence. In the axes, the ureides were almost equally distributed in roots, hypocotyls and epicotyls. The pattern of ureide distribution was not affected by the presence of nitrate or sucrose in the media up to 6 days after imbibition. Ureides are synthesized from purines because allopurinol (a xanthine dehydrogenase inhibitor) blocks the increase of ureides. Allantoin and allantoate-degrading activities were detected in French bean dried seeds, whereas no ureidoglycolate-degrading activity was detected. During germination, the levels of the three activities remain unchanged in cotyledons. After radicle emergence, the levels of activities in cotyledons changed. Allantoin-degrading activity increased, allantoate-degrading activity decreased and ureidoglycolate-degrading activity remained undetectable in cotyledons. In developing embryonic axes, the three activities were detected throughout germination and early seedling development. The embryonic axes are able to synthesize ureides, because those compounds accumulated in axes without cotyledons.

Expression of ABA 8'-hydroxylases in relation to leaf water relations and seed development in bean.

In plants, the level of abscisic acid (ABA) is determined by synthesis and catabolism. Hydroxylation of ABA at the 8' position is the key step in ABA catabolism. This reaction is catalyzed by ABA 8'-hydroxylase, a cytochrome P450 (CYP). The cDNAs of PvCYP707A1 and PvCYP707A2 were isolated from bean (Phaseolus vulgaris L.) axes treated with (+)-ABA and that of PvCYP707A3 from dehydrated bean leaves. The recombinant PvCYP707A proteins expressed in yeast were biochemically characterized. Yeast strains over-expressing any of the three PvCYP707As were able to convert ABA to phaseic acid (PA). The microsomal fractions from these yeast strains also exhibited ABA 8'-hydroxylase activity. Expression of PvCYP707A3 in primary leaves was strongly increased by water stress, whereas PvCYP707A1 and PvCYP707A2 mRNA levels were rapidly increased by rehydration of water-stressed leaves. Northern blot analysis of PvCYP707As in bean showed a high level of expression in the mature fruits, senescent leaves, roots, seed coats and axes. All three PvCYP707As were expressed at varying intensities throughout seed development. Imbibed seeds also had high PvCYP707A mRNA levels. Thus, expression of PvCYP707As is both environmentally and developmentally regulated. Transgenic Nicotiana sylvestris plants over-expressing PvCYP707As displayed a wilty phenotype, and had reduced ABA levels and increased PA levels. These results demonstrate that expression of PvCYP707As is the major mechanism by which ABA catabolism is regulated in bean.

In vitro somatic embryogenesis from cell suspension cultures of cowpea [Vigna unguiculata (L.) Walp].

We report, an efficient protocol for plantlet regeneration from the cell suspension cultures of cowpea through somatic embryogenesis. Primary leaf-derived, embryogenic calli initiated in MMS [MS salts (Murashige and Skoog 1962) with B5 (Gamborg et al. 1968) vitamins] medium containing 2,4-Dichlorophenoxyacetic acid (2,4-D), casein hydrolysate (CH), and L: -Glutamic acid-5-amide (Gln). Fast-growing embryogenic cell suspensions were established in 0.5 mg l(-1) 2,4-D, which resulted in the highest recovery of early stages of somatic embryos in liquid MMS medium. Embryo development was asynchronous and strongly influenced by the 2,4-D concentration. Mature monocotyledonary-stage somatic embryos were induced in liquid B5 medium containing 0.1 mg l(-1) 2,4-D, 20 mg l(-1) L: -Proline (Pro), 5 muM Abscisic acid (ABA), and 2% mannitol. B5 medium was found superior for the maturation of somatic embryos compared to MS and MMS media. The importance of duration (5 d) for effective maturation of somatic embryos is demonstrated. A reduction in the 2,4-D level in suspensions increased the somatic embryo induction and maturation with decreased abnormalities. Sucrose was found to be the best carbon source for callus induction while mannitol for embryo maturation and maltose for embryo germination. Extension of hypocotyls and complete development of plantlet was achieved in half-strength B5 medium supplemented with 3% maltose, 2500 mg l(-1) potassium nitrate, and 0.05 mg l(-1) thidiazuron (TDZ) with 32% regeneration frequency. Field-established plants were morphologically normal and fertile. This regeneration protocol assures a high frequency of embryo induction, maturation, and plantlet conversion.

Expression of two genes encoding gibberellin 2- and 3-oxidases in developing seeds of Phaseolus coccineus.

We have isolated PcGA3ox1, a cDNA clone from developing runner bean (Phaseolus coccineus) seeds that shows significant amino acid homology with the gibberellin (GA) 3-oxidases. A recombinant fusion protein of PcGA3ox1 converted GA20 and GA9 to GA1 and GA4, respectively. In situ hybridization results showed that transcripts of this gene accumulate specifically within the suspensor of globular-stage embryos. PcGA3ox1 mRNA begins to accumulate in the epidermal cells of the embryo proper and is also detectable in the endosperm during the transition from globular- to heart-stage embryos. PcGA3ox1 transcripts were localized exclusively in the cotyledons from the early cotyledonary stage up to the cotyledonary stage. Transcripts of the previously cloned GA 2-oxidase (PcGA2ox1) from developing seeds of runner bean were found primarily within the suspensor neck region from the late globular stage up to the heart stage. PcGA2ox1 mRNA was detectable in the whole suspensor from the early cotyledonary stage, and was found in the inner layer of integuments at the cotyledonary stage. Soluble enzyme preparations made from suspensors and embryos at two stages of embryogenesis (the heart and cotyledonary stages) were incubated with [14C]GA20 and [14C]GA1. Only young suspensor preparations converted GA20 to GA1 and GA5. Both suspensor preparations converted GA1 to GA8. Both embryo preparations converted GA20 to GA1, but were unable to convert GA1 to GA8.

Characterization of a novel acid phosphatase from embryonic axes of kidney bean exhibiting vanadate-dependent chloroperoxidase activity.

A novel colorless acid phosphatase (KeACP), which was distinct from the kidney bean purple acid phosphatase, was purified to apparent homogeneity and cloned from embryonic axes of kidney bean (Phaseolus vulgaris L. Ohfuku) during germination. When orthovanadate (VO(4)(-3)) is added to the apo form of the enzyme, KeACP uniquely exhibits the chloroperoxidase activity with loss of phosphatase activity. This is the first demonstration that KeACP is a vanadate-dependent chloroperoxidase in plants to be characterized and suggests that KeACP may play a role in modifying a wide variety of chlorinated compounds that are present in higher plants. The enzyme is a dimer that presents three forms made up of the combination of the dominant 56-kDa and the minor 45-kDa subunits, and both subunits contain carbohydrate. The full-length cDNA of the KeACP gene is 1641 nucleotides, and this sequence is predicted to encode a protein having 457 amino acid residues (52,865 Da), including a signal peptide. The complete nucleotide sequence of the genomic DNA (3228 bp) of KeACP consists of seven exons and six introns. Northern blot analysis demonstrated that the KeACP gene was expressed specifically in embryonic axes of the kidney bean, and its expression coincided with elongation of the embryonic axis during germination.